7DOD | pdb_00007dod

Capsid structure of human sapovirus

PDB DOI: https://doi.org/10.2210/pdb7DOD/pdb
EM Map EMD-30793: EMDB EMDataResource

Classification: VIRUS
Organism(s): Sapovirus Hu/GI.6/Nichinan/FP05284/2005/JPN
Expression System: Baculovirus expression vector pFastBac1-HM
Mutation(s): No

Deposited: 2020-12-14 Released: 2021-12-15
Deposition Author(s): Miyazaki, N., Murakami, K., Oka, T., Iwasaki, K., Katayama, K., Murata, K.
Funding Organization(s): Japan Agency for Medical Research and Development (AMED), Ministry of Education, Culture, Sports, Science and Technology (Japan)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 2.90 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

Validation slider image for 7DOD

This is version 1.2 of the entry. See complete history.

Literature

Atomic structure of human sapovirus capsid by single particle cryo-electron microscopy

Miyazaki, N., Murakami, K., Oka, T., Iwasaki, K., Katayama, K., Murata, K.

To be published.

Macromolecule Content

Total Structure Weight: 182.26 kDa
Atom Count: 11,916
Modeled Residue Count: 1,573
Deposited Residue Count: 1,695
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Calicivirin	A [auth C], B [auth A], C [auth B]	565	Sapovirus Hu/GI.6/Nichinan/FP05284/2005/JPN	Mutation(s): 0

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 2.90 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX
RECONSTRUCTION	RELION

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2021-12-15

Deposition Author(s):

Funding Organization	Location	Grant Number
Japan Agency for Medical Research and Development (AMED)	Japan	20fk0108121h0402
Ministry of Education, Culture, Sports, Science and Technology (Japan)	Japan	JP16H00786

Revision History (Full details and data files)

Version 1.0: 2021-12-15
Type: Initial release
Version 1.1: 2024-06-05
Changes: Data collection, Derived calculations
Version 1.2: 2025-07-02
Changes: Data collection, Structure summary

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.